Hi Katarina, To find out the format of any file, go into the Table browser, set the appropriate clade, genome, release, track group, track, and finally table. Then click on "View table schema". This will take you to a page that lists the table schema, data types, example lines, and related or linked tables/files (and what key is the link).
For the phastConsElements4way table, I get this result using hg18: Database: hg18 Primary Table: phastConsElements44way Row Count: 4,878,296 Format description: Browser extensible data field example SQL type description bin 585 smallint(5)unsigned Indexing field to speed chromosome range queries. chrom chr1 varchar(255) Reference sequence chromosome or scaffold chromStart 1865 int(10)unsigned Start position in chromosome chromEnd 1948 int(10)unsigned End position in chromosome name lod=23 varchar(255) Name of item score 304 int(10)unsigned Score from 0-1000 The first column (bin) is a database indexing number we use. Ignore or cut it out of your file. The last column (score) is more complicated to explain, but in general, the higher the score, the better the conservation. Instead of me listing all the details here, go to the track description by scrolling down on the "View table schema" page (or linking through the track name in the assembly's browser) to the section titled "PhastCons Conservation". Hope we helped again. For the fastest response to an answer, please send all questions (including follow-up questions) directly to the mailing list unless data was specifically requested to be send privately, Thank you! Jennifer Jackson UCSC Genome Bioinformatics Group > Hi Jennifer, > Thanks a lot! I think I found the file I was looking for, but I would > be happy if you could explain what I see in the first and last column. > I found the file > at http://hgdownload.cse.ucsc.edu/goldenPath/canFam2/database/ > <http://hgdownload.cse.ucsc.edu/goldenPath/canFam2/database/> > and the name of the file is phastConsElements4way.txt > Thanks > Katarina > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
